Merge branch 'add_notebooks' into 'main'

Add notebooks

See merge request !75

est/core/process/energyroi.py

@@ -13,8 +13,9 @@ def xas_energy_roi(xas_obj):
     :return: spectra dict
     :rtype: :class:`.XASObject`
     """
-    xas_roi_process = EnergyROIProcess(inputs={"xas_obj": xas_obj})
-    return xas_roi_process.run()
+    process = EnergyROIProcess(inputs={"xas_obj": xas_obj})
+    process.run()
+    return process.get_output_value("xas_obj", None)
 
 
 class EnergyROIProcess(
@@ -51,7 +52,6 @@ class EnergyROIProcess(
 
         self.register_process(_xas_obj, data_keys=("Mu", "energy"))
         self.outputs.xas_obj = _xas_obj  # .to_dict()
-        return _xas_obj
 
     def _apply_roi(self, xas_obj, emin, emax):
         if emin is None and emax is None:

est/core/process/io.py

@@ -51,4 +51,3 @@ class ReadXasObject(
         input_information = InputInformation.from_dict(self.inputs.input_information)
         xas_obj = XASReader.read_frm_url(input_information)
         self.outputs.xas_obj = xas_obj
-        return xas_obj

est/core/process/larch/autobk.py

@@ -90,7 +90,7 @@ def process_spectr_autobk(
     return configuration, _spectrum
 
 
-def larch_autobk(xas_obj, config: dict):
+def larch_autobk(xas_obj, **optional_inputs):
     """
 
     :param xas_obj: object containing the configuration and spectra to process
@@ -98,8 +98,9 @@ def larch_autobk(xas_obj, config: dict):
     :return: spectra dict
     :rtype: XASObject
     """
-    mback_obj = Larch_autobk(inputs={"xas_obj": xas_obj, "autobk_config": config})
-    return mback_obj.run()
+    process = Larch_autobk(inputs={"xas_obj": xas_obj, **optional_inputs})
+    process.run()
+    return process.get_output_value("xas_obj", None)
 
 
 class Larch_autobk(
@@ -118,7 +119,6 @@ class Larch_autobk(
         self.progress = 100
         self.register_process(_xas_obj, data_keys=(_NexusDatasetDef("bkg"),))
         self.outputs.xas_obj = _xas_obj  # .to_dict()
-        return _xas_obj
 
     def _pool_process(self, xas_obj):
         assert isinstance(xas_obj, XASObject)
@@ -144,5 +144,3 @@ class Larch_autobk(
     @staticmethod
     def program_name():
         return "larch_autobk"
-
-    __call__ = run

est/core/process/larch/mback.py

@@ -81,7 +81,7 @@ def process_spectr_mback(
     return configuration, _spectrum
 
 
-def larch_mback(xas_obj, config: dict):
+def larch_mback(xas_obj, **optional_inputs):
     """
 
     :param xas_obj: object containing the configuration and spectra to process
@@ -89,8 +89,9 @@ def larch_mback(xas_obj, config: dict):
     :return: spectra dict
     :rtype: XASObject
     """
-    mback_obj = Larch_mback(inputs={"xas_obj": xas_obj, "mback_config": config})
-    return mback_obj.run()
+    process = Larch_mback(inputs={"xas_obj": xas_obj, **optional_inputs})
+    process.run()
+    return process.get_output_value("xas_obj", None)
 
 
 class Larch_mback(
@@ -115,7 +116,6 @@ class Larch_mback(
             ),
         )
         self.outputs.xas_obj = _xas_obj  # .to_dict()
-        return _xas_obj
 
     def _pool_process(self, xas_obj):
         assert isinstance(xas_obj, XASObject)
@@ -141,5 +141,3 @@ class Larch_mback(
     @staticmethod
     def program_name():
         return "larch_mback"
-
-    __call__ = run

est/core/process/larch/mback_norm.py

@@ -87,7 +87,7 @@ def process_spectr_mback_norm(
     return configuration, _spectrum
 
 
-def larch_mback_norm(xas_obj, config: dict):
+def larch_mback_norm(xas_obj, **optional_inputs):
     """
 
     :param xas_obj: object containing the configuration and spectra to process
@@ -95,10 +95,9 @@ def larch_mback_norm(xas_obj, config: dict):
     :return: spectra dict
     :rtype: XASObject
     """
-    mback_obj = Larch_mback_norm(
-        inputs={"xas_obj": xas_obj, "mback_norm_config": config}
-    )
-    return mback_obj.run()
+    process = Larch_mback_norm(inputs={"xas_obj": xas_obj, **optional_inputs})
+    process.run()
+    return process.get_output_value("xas_obj", None)
 
 
 class Larch_mback_norm(
@@ -123,7 +122,6 @@ class Larch_mback_norm(
             data_keys += ["norm"]
         self.register_process(_xas_obj, data_keys=data_keys)
         self.outputs.xas_obj = _xas_obj  # .to_dict()
-        return _xas_obj
 
     def _pool_process(self, xas_obj):
         assert isinstance(xas_obj, XASObject)
@@ -149,5 +147,3 @@ class Larch_mback_norm(
     @staticmethod
     def program_name():
         return "larch_mback_norm"
-
-    __call__ = run

est/core/process/larch/pre_edge.py

@@ -87,7 +87,7 @@ def process_spectr_pre_edge(
     return configuration, _spectrum
 
 
-def larch_pre_edge(xas_obj, config: dict):
+def larch_pre_edge(xas_obj, **optional_inputs):
     """
 
     :param xas_obj: object containing the configuration and spectra to process
@@ -95,8 +95,9 @@ def larch_pre_edge(xas_obj, config: dict):
     :return: spectra dict
     :rtype: XASObject
     """
-    mback_obj = Larch_pre_edge(inputs={"xas_obj": xas_obj, "pre_edge_config": config})
-    return mback_obj.run()
+    process = Larch_pre_edge(inputs={"xas_obj": xas_obj, **optional_inputs})
+    process.run()
+    return process.get_output_value("xas_obj", None)
 
 
 class Larch_pre_edge(
@@ -177,7 +178,6 @@ class Larch_pre_edge(
             ),
         )
         self.outputs.xas_obj = _xas_obj  # .to_dict()
-        return _xas_obj
 
     def _pool_process(self, xas_obj):
         assert isinstance(xas_obj, XASObject)
@@ -203,5 +203,3 @@ class Larch_pre_edge(
     @staticmethod
     def program_name():
         return "larch_pre_edge"
-
-    __call__ = run

est/core/process/larch/xftf.py

@@ -114,7 +114,7 @@ def process_spectr_xftf(
     return configuration, _spectrum
 
 
-def larch_xftf(xas_obj, config: dict):
+def larch_xftf(xas_obj, **optional_inputs):
     """
 
     :param xas_obj: object containing the configuration and spectra to process
@@ -122,8 +122,9 @@ def larch_xftf(xas_obj, config: dict):
     :return: spectra dict
     :rtype: XASObject
     """
-    mback_obj = Larch_xftf(inputs={"xas_obj": xas_obj, "xftf_config": config})
-    return mback_obj.run()
+    process = Larch_xftf(inputs={"xas_obj": xas_obj, **optional_inputs})
+    process.run()
+    return process.get_output_value("xas_obj", None)
 
 
 class Larch_xftf(
@@ -203,7 +204,6 @@ class Larch_xftf(
             ),
         )
         self.outputs.xas_obj = _xas_obj  # .to_dict()
-        return _xas_obj
 
     def _pool_process(self, xas_obj):
         assert isinstance(xas_obj, XASObject)
@@ -229,5 +229,3 @@ class Larch_xftf(
     @staticmethod
     def program_name():
         return "larch_xftf"
-
-    __call__ = run

est/core/process/noise.py

@@ -156,5 +156,3 @@ class NoiseProcess(
     @staticmethod
     def program_name():
         return "noise_savgol"
-
-    __call__ = run

est/core/process/pymca/exafs.py

@@ -97,7 +97,7 @@ def process_spectr_exafs(
     return configuration, get_output(spectrum, res_spectrum)
 
 
-def pymca_exafs(xas_obj):
+def pymca_exafs(xas_obj, **optional_inputs):
     """
 
     :param xas_obj: object containing the configuration and spectra to process
@@ -105,8 +105,9 @@ def pymca_exafs(xas_obj):
     :return: spectra dict
     :rtype: XASObject
     """
-    exafs_obj = PyMca_exafs(inputs={"xas_obj": xas_obj})
-    return exafs_obj.run()
+    process = PyMca_exafs(inputs={"xas_obj": xas_obj, **optional_inputs})
+    process.run()
+    return process.get_output_value("xas_obj", None)
 
 
 class PyMca_exafs(
@@ -144,7 +145,6 @@ class PyMca_exafs(
             ),
         )
         self.outputs.xas_obj = _xas_obj  # .to_dict()
-        return _xas_obj
 
     def _pool_process(self, xas_obj):
         assert isinstance(xas_obj, XASObject)
@@ -171,5 +171,3 @@ class PyMca_exafs(
     @staticmethod
     def program_name():
         return "pymca_exafs"
-
-    __call__ = run

est/core/process/pymca/ft.py

@@ -101,7 +101,7 @@ def process_spectr_ft(
     return configuration, spectrum_
 
 
-def pymca_ft(xas_obj):
+def pymca_ft(xas_obj, **optional_inputs):
     """
 
     :param xas_obj: object containing the configuration and spectra to process
@@ -109,9 +109,9 @@ def pymca_ft(xas_obj):
     :return: spectra dict
     :rtype: dict
     """
-    assert xas_obj is not None
-    ft_obj = PyMca_ft(inputs={"xas_obj": xas_obj})
-    return ft_obj.run()
+    process = PyMca_ft(inputs={"xas_obj": xas_obj, **optional_inputs})
+    process.run()
+    return process.get_output_value("xas_obj", None)
 
 
 class PyMca_ft(
@@ -158,7 +158,6 @@ class PyMca_ft(
             ),
         )
         self.outputs.xas_obj = _xas_obj  # .to_dict()
-        return _xas_obj
 
     def _pool_process(self, xas_obj):
         assert isinstance(xas_obj, XASObject)
@@ -183,5 +182,3 @@ class PyMca_ft(
     @staticmethod
     def program_name():
         return "pymca_ft"
-
-    __call__ = run

est/core/process/pymca/k_weight.py

@@ -90,7 +90,7 @@ def process_spectr_k(
     return configuration_, spectrum_
 
 
-def pymca_k_weight(xas_obj):
+def pymca_k_weight(xas_obj, **optional_inputs):
     """
     Set weight for exafs values
 
@@ -99,8 +99,9 @@ def pymca_k_weight(xas_obj):
     :return: spectra dict
     :rtype: :class:`.XASObject`
     """
-    k_weight_obj = PyMca_k_weight(inputs={"xas_obj": xas_obj})
-    return k_weight_obj.run()
+    process = PyMca_k_weight(inputs={"xas_obj": xas_obj, **optional_inputs})
+    process.run()
+    return process.get_output_value("xas_obj", None)
 
 
 class PyMca_k_weight(
@@ -160,7 +161,6 @@ class PyMca_k_weight(
         self.progress = 100.0
         self.register_process(xas_obj=_xas_obj, data_keys=tuple())
         self.outputs.xas_obj = _xas_obj  # .to_dict()
-        return _xas_obj
 
     def _pool_process(self, xas_obj):
         """process normalization from a pool"""
@@ -188,5 +188,3 @@ class PyMca_k_weight(
     @staticmethod
     def program_name():
         return "pymca_k_weight"
-
-    __call__ = run

est/core/process/pymca/normalization.py

@@ -75,7 +75,7 @@ def process_spectr_norm(
     return configuration, get_output(spectrum, spectrum_)
 
 
-def pymca_normalization(xas_obj):
+def pymca_normalization(xas_obj, **optional_inputs):
     """
 
     :param xas_obj: object containing the configuration and spectra to process
@@ -84,8 +84,9 @@ def pymca_normalization(xas_obj):
     :return: spectra dict
     :rtype: dict
     """
-    normalization_obj = PyMca_normalization(inputs={"xas_obj": xas_obj})
-    return normalization_obj.run()
+    process = PyMca_normalization(inputs={"xas_obj": xas_obj, **optional_inputs})
+    process.run()
+    return process.get_output_value("xas_obj", None)
 
 
 class PyMca_normalization(
@@ -133,9 +134,7 @@ class PyMca_normalization(
                 _NexusDatasetDef("NormalizedSignal"),
             ),
         )
-        xas_obj_as_dict = _xas_obj.to_dict()
-        self.outputs.xas_obj = xas_obj_as_dict
-        return _xas_obj
+        self.outputs.xas_obj = _xas_obj  # .to_dict()
 
     def _pool_process(self, xas_obj):
         """process normalization from a pool"""
@@ -161,5 +160,3 @@ class PyMca_normalization(
     @staticmethod
     def program_name():
         return "pymca_normalization"
-
-    __call__ = run

est/core/process/roi.py

@@ -19,8 +19,9 @@ def xas_roi(xas_obj):
     :return: spectra dict
     :rtype: :class:`.XASObject`
     """
-    xas_roi_process = ROIProcess(inputs={"xas_obj": xas_obj})
-    return xas_roi_process.run()
+    process = ROIProcess(inputs={"xas_obj": xas_obj})
+    process.run()
+    return process.get_output_value("xas_obj", None)
 
 
 class _ROI:
@@ -162,10 +163,7 @@ class ROIProcess(
             origin, size = roi_dict["origin"], roi_dict["size"]
             _xas_obj = self._apply_roi(xas_obj=_xas_obj, roi=_ROI(origin, size))
         self.outputs.xas_obj = _xas_obj  # .to_dict()
-        return _xas_obj
 
     @staticmethod
     def program_name():
         return "roi"
-
-    __call__ = run

est/tests/larch/test_autobk.py

@@ -34,7 +34,7 @@ def xas_object(spectrum_cu_from_larch):
 @pytest.mark.skipif(larch is None, reason="xraylarch not installed")
 def test_multiple_spectra(xas_object):
     """Make sure computation on spectra is valid (n spectrum)"""
-    res = larch_autobk(xas_object, {})
+    res = larch_autobk(xas_object)
     assert isinstance(res, XASObject)
     spectrum0 = res.spectra.data.flat[0]
     assert hasattr(spectrum0, "k")
@@ -44,7 +44,7 @@ def test_multiple_spectra(xas_object):
 @pytest.mark.skipif(larch is None, reason="xraylarch not installed")
 def test_multiple_spectra_as_dict(xas_object):
     """Make sure computation on spectra is valid (n spectrum)"""
-    res = larch_autobk(xas_object.to_dict(), {})
+    res = larch_autobk(xas_object.to_dict())
     assert isinstance(res, XASObject)
     spectrum0 = res.spectra.data.flat[0]
     assert hasattr(spectrum0, "k")

est/tests/larch/test_mback.py

@@ -35,7 +35,7 @@ def xas_object(spectrum_cu_from_larch):
 @pytest.mark.skipif(larch is None, reason="xraylarch not installed")
 def test_multiple_spectra(xas_object):
     """Make sure computation on spectra is valid (n spectrum)"""
-    res = larch_mback(xas_object, {"z": 29})
+    res = larch_mback(xas_object, mback_config={"z": 29})
     assert isinstance(res, XASObject)
     spectrum0 = res.spectra.data.flat[0]
     assert hasattr(spectrum0, "fpp")
@@ -45,7 +45,7 @@ def test_multiple_spectra(xas_object):
 @pytest.mark.skipif(larch is None, reason="xraylarch not installed")
 def test_multiple_spectra_asdict(xas_object):
     """Make sure computation on spectra is valid (n spectrum)"""
-    res = larch_mback(xas_object.to_dict(), {"z": 29})
+    res = larch_mback(xas_object.to_dict(), mback_config={"z": 29})
     assert isinstance(res, XASObject)
     spectrum0 = res.spectra.data.flat[0]
     assert hasattr(spectrum0, "fpp")

est/tests/larch/test_mback_norm.py

@@ -48,7 +48,7 @@ def xas_object(spectrum_cu_from_larch):
 @pytest.mark.skipif(larch is None, reason="xraylarch not installed")
 def test_multiple_spectra(xas_object):
     """Make sure computation on spectra is valid (n spectrum)"""
-    res = larch_mback_norm(xas_object, {})
+    res = larch_mback_norm(xas_object)
     assert isinstance(res, XASObject)
     spectrum0 = res.spectra.data.flat[0]
     assert hasattr(spectrum0, "mback_mu")
@@ -58,7 +58,7 @@ def test_multiple_spectra(xas_object):
 @pytest.mark.skipif(larch is None, reason="xraylarch not installed")
 def test_multiple_spectra_asdict(xas_object):
     """Make sure computation on spectra is valid (n spectrum)"""
-    res = larch_mback_norm(xas_object.to_dict(), {})
+    res = larch_mback_norm(xas_object.to_dict())
     assert isinstance(res, XASObject)
     spectrum0 = res.spectra.data.flat[0]
     assert hasattr(spectrum0, "mback_mu")

est/tests/larch/test_pre_edge.py

@@ -35,7 +35,7 @@ def xas_object(spectrum_cu_from_larch):
 @pytest.mark.skipif(larch is None, reason="xraylarch not installed")
 def test_multiple_spectra(xas_object):
     """Make sure computation on spectra is valid (n spectrum)"""
-    res = larch_pre_edge(xas_object, {})
+    res = larch_pre_edge(xas_object)
     assert isinstance(res, XASObject)
     spectrum0 = res.spectra.data.flat[0]
     assert hasattr(spectrum0, "pre_edge")
@@ -45,7 +45,7 @@ def test_multiple_spectra(xas_object):
 @pytest.mark.skipif(larch is None, reason="xraylarch not installed")
 def test_multiple_spectra_asdict(xas_object):
     """Make sure computation on spectra is valid (n spectrum)"""
-    res = larch_pre_edge(xas_object.to_dict(), {})
+    res = larch_pre_edge(xas_object.to_dict())
     assert isinstance(res, XASObject)
     spectrum0 = res.spectra.data.flat[0]
     assert hasattr(spectrum0, "pre_edge")

est/tests/larch/test_xftf.py

@@ -53,7 +53,7 @@ def xas_object(spectrum_cu_from_larch):
 @pytest.mark.skipif(larch is None, reason="xraylarch not installed")
 def test_multiple_spectra(xas_object):
     """Make sure computation on spectra is valid (n spectrum)"""
-    res = larch_xftf(xas_object, {})
+    res = larch_xftf(xas_object)
     assert isinstance(res, XASObject)
     spectrum = res.spectra.data.flat[0]
     assert hasattr(spectrum, "chir_re")
@@ -65,7 +65,7 @@ def test_multiple_spectra(xas_object):
 @pytest.mark.skipif(larch is None, reason="xraylarch not installed")
 def test_multiple_spectra_asdict(xas_object):
     """Make sure computation on spectra is valid (n spectrum)"""
-    res = larch_xftf(xas_object.to_dict(), {})
+    res = larch_xftf(xas_object.to_dict())
     assert isinstance(res, XASObject)
     spectrum = res.spectra.data.flat[0]
     assert hasattr(spectrum, "chir_re")